Mass Effect 3: A New Ally, or Enemy?
by shifty53
Summary: The Irken Fleet was found in the Milky Way galaxy. Commander Shepard was sent to investigate Cerburus using completely unknown technology only to discover the location of the Irken Armada. Commander Shepard makes a deal with the Tallest to take one of their most dangerous and annoying operatives in exchange for support. How bad could this operative really be?
1. Chapter 1

**This story will take place with default male Shepard (mostly paragon with some renegade)**

**Shepard is in a relationship with Tali in this story. If someone wants an alternate version of this story just ask! ;)**

**Anyone familiar with Mass Effect will know what I'm talking about above. This story takes place during the events of ME3. Mass Effect belongs to Bioware, and Invader Zim belongs to Jhonen Vasquez.  
**

The Cerberus troops shambled across the torn up battlefield of Firebase Jade to try to at the least hold back Commander Shepard. Just a few hours ago admiral Hackett informed Shepard that Cerberus was using some form of unknown technology. Possibly reaper, or maybe something else.

An injured Cerberus Centurion limped into cover and activated his communicator. He coughed and then began to speak. "We failed. Send in the new experiments." The Centurion then pulled a gun up to his head and shot himself.

Shepard, Javik, and Garrus wiped out the last of the Cerberus troops. "Commander! There are more heading our way!" shouted Javik. A Cerburus shuttle flew onto the battlefield. As it opened Shepard noticed some unusual looking troops. At first they appeared to be phantoms, but it was soon clear they were too short to be phantoms. They also had antennae which Shepard thought was very strange.

Garrus fired a concussive shot knocking one of them off the shuttle but they soon scattered and were moving very quickly across the battlefield. Shepard and his team struggled to hit any of the strange new enemies as they darted across the battlefield firing powerful weapons Shepard had never seen before.

Garrus managed to hit a lot of them with his Black Widow sniper rifle, but Shepard and Javik struggled because they had particle rifles. They managed to melt a few but not many of the strange creatures. Eventually they had all been eradicated. Garrus got most of them and bragged about it while the team searched for the unknown tech that was reported.

"This must be the kind of tech were looking for." said Shepard as he picked up a strange purple rifle with strange symbols on it. After a few minutes of searching Shepard and his team found a door that could be bypassed.

Shepard quickly bypassed the doors security and went in to see what was hidden behind the door. The room was filled with purple technology and strange symbols much like the gun Shepard recovered. "Well maybe we'll get lucky and Leviathen can explain all this crap." Said Garrus in his usual sarcastic tone.

Shepard picked up a small device and examined it for awhile but eventually stored it away. "Sorry Garrus. This is not from Leviathen's race, or any race we've ever seen before." Said Shepard. "Shepard. Look at this." Said Garrus .

Garrus was standing behind one of the computers looking at an extremely large fleet of ships with a massive flagship in the center. "Garrus copy these files to our omni-tools. We'll need to trace where they're coming from later.

"Hey. The screen just turned red and started to beep. Oh shit, that can only mean one thing." Said Garrus. Shepard looked at the monitor then shouted to his team. "RUN!" Shepard and his team ran out of the purple room and dived to the ground just outside of the room just as it exploded.

Later on the Normandy Shepard spoke to admiral Hackett about what they found. "So we have records of a large fleet that could either wipe out the reapers or wipe us out, and a very powerful new gun. This is race we've never seen before. It seems they usually operate outside of the Milky Way but for some reason they've shown up here and Ceberus has captured and repurposed some of their soldiers. This is too big to ignore Shepard. You have to try to get their support. Hackett out."

So with that, the Normandy traveled to where the strange fleet was last located. In the meantime Shepard headed down to engineering to talk to Tali about the recent events. "I don't know Shepard. A fleet that powerful. We don't even know what they want. I think it's too dangerous."

"Tali. We need anything we can to help fight the reapers. I know your worried about this, so am I. There is no telling what a ship that size could do. But if they are interested in helping us, we'll have the reapers backed into a corner. We'll finally be able to start going on the offensive in this war while the crucible is being built." Said Shepard.

"I don't know Shepard, just please be careful. Your really pushing it you know, almost getting yourself killed while going after Leviathen now this. You better not die on me." Said Tali. "Don't worry. I won't." said Shepard giving Tali a comforting hug as he said that.

Shepard went to get Javik's opinion on the topic, expecting his usually negative view on things. He'd probably say he needed to destroy the fleet. Javik was washing his hands like he always did when Shepard walked in. "Ah commander. This fleet we've found. It could potentially kill thousands of reapers. I think you should find a way to fool these things and throw them at the reapers. We don't know them, they don't know us. Their casualties would not matter."

Shepard wanted to talk but said nothing and headed back up to deck two. "Commander. We're getting a transmission from the flagship. Looks like it's only compatible in video form. Patching it through." Said Joker.

A large monitor came down above the galaxy map. Shepard had never seen it before. Must have been one of the lesser improvements made to the Normandy, Shepard thought. Two green figures with antennae, one with red eyes, the other with purple eyes appeared on the screen.

"What the-? A human? We haven't seen humans in almost 200 years." Said the Purple eyed creature. "I'm Commander Shepard of the human alliance vessel, Normandy SR2. We're at war right now with something we call, the reapers. They come to our galaxy every 50,000 years to extinguish all life."

"Wow that's, really weird. Well the _reapers _as you call them have been giving us trouble as well. Our homeworld, Irk was taken, despite the fact that it's not even in your galaxy. So we've decided to attack the reapers in this galaxy. That's all we will say over this channel." Said the red eyed creature.

"Well there is a place aboard my ship where we can discuss this." Replied Shepard. "Okay human, but don't blame us for bringing guards, we don't exactly trust you." Said the red eyed creature.

The large flagship then docked the Normandy and a few of the creatures with weapons guarded the two tallest of the creatures. "Ah hello Commander. Well I think I should explain what we are and the way our race operates. We are the Irkens. We conquered about three galaxies outside of yours. I am Tallest Red and my partner here is Tallest Purple. Our race chooses it's leaders based on height. Well that's pretty much it. We also clone all of our troops giving us a very large amount of soldiers. That big ship out there, it's called the Massive. Every Irken also has a PAK which functions as most of our brain and life support."

"Well we have plans for a device that could potentially wipe out the reapers in our galaxy. I'm not sure if the blast from our weapon would reach your planet but if you could use the Massive to point one of the Mass Relays in our galaxy towards your planet I think that the blast may be shot to your planet. I'm not sure though."

"Hmm. Let me see the plans for this device." Asked Tallest Red. Shepard then pulled up a hologram of the crucible. "Well that other human who asked for our help doesn't have this. It sure looks like it could destroy the reapers." Said Tallest Purple.

"Wait someone else asked for your help?" asked Shepard. "Yes. He called himself The Illusive Man. He runs something called Cerberus. When we declined helping him he began to abduct our Irken Elite soldiers, so that's why we don't exactly trust humans." Said Tallest Red.

"Well, what exactly would it take to get your support in building the crucible and with fighting the reapers?" asked Shepard. "Well, we do need someone to help rescue some of our Irken Elites from reaper and Cerberus forces. But most importantly, we need you to take someone off our back." Said Tallest Red.

"What do you mean like, a soldier or something?" asked Shepard. "You could say that. But you can use him as a shield for all we care, we just need him out of our hands. We've kept him in a stasis pod for almost 200 years when we deemed it would be to dangerous to simply keep him as a prisoner." Said Tallest Red.

"Dangerous? Just how dangerous is this person you're telling me about?" asked Shepard. "Well, uh... you see he's_ very_ unpredictable and has caused us a lot of trouble." Said Tallest Red. "You should also take anger management before you meet him because he can be, well let's just say he'll give you a headache." Said Tallest Purple.

"Well I'll take him if that's what it takes to get you to help us. I mean he can't be that bad, can he?" Said Shepard. "Oh if you only knew. Well you don't even have to take him out of that stasis pod he's in but you just need to keep him as far away from us as you can. And please, try to get him killed." Said Tallest Red as Him and Purple got up to leave.

Soon after, two Irken soldiers brought the pod onto the Normandy. Shepard pointed them to the elevator and they brought the pod to engineering and placed it in port cargo with Javik on the far side of the room away from Javik.

Shepard looked at the pod for a minute. It had Irken symbols on it which appeared to be a warning. Shepard could see nothing inside the pod but could tell by it's size that it contained something very short. "Javik. Can you tell me anything about what's inside this pod?" Asked Shepard.

Javik walked over to the pod and looked at it for a moment before resting his hands on it and closing his four eyes. Javik quickly snapped away from the pod in shock. "I sense much frustration and anger. Whatever is in there is insane and has no understanding for anything it sees." Said Javik.

Shepard sighed. "Well thanks anyway Javik" said Shepard. "Commander." Javik said returning to washing his hands. Shepard looked at the pod once more. He saw a button on the side. He pressed it and a hologram of warnings in the Irken language appeared and Shepard ignored them and pressed the button again.

The pod began to make whirring sounds and blast out steam. "Commander. You have made a grave mistake." Said Javik. Finally the pod opened and a small Irken emerged. Shepard looked at it for a moment.

The small Irken looked around for a moment then suddenly a evil look went over it's face and it began to speak. "I AM ZIM!"

**Well theres the end to chapter 1. Remember if you want an alternated version with a different Shepard just leave your request in the reviews or if you have an account then P.M. me. Hope you all enjoyed. Let me know what you think! **


	2. Chapter 2: Zim's awakening

**A.N.**

**Well Zim's awake. Too late now Shepard! Oh he will seriously regret waking up Zim. **

Zim sat in his pod and continued to scream no for about five minutes. "Hey, can you just calm down. We have a war to fight and I'm going to need your help." Said Shepard. "Neat. What are we fighting? Humans? Well in that case I'll start with you." Said Zim.

"No! We're fighting the reapers." Said Shepard. "The giant burrito monsters? But they were never any problem before." "Well they're trying to kill all organic life in our galaxy." "Oh well, I don't care." As Zim said that he stood up and walked to the other side of the room.

He bumped into Javik and the prothean shot him a glare. Zim screamed at the sight of Javik and ran back towards Shepard. "I'm your Commander. You can call me Shepard, and that's Javik over there, I'd explain his story to you but something tells me you wouldn't understand."

"If that Javik _thing_ looks at me again I'll destroy it!" said Zim. "No you won't Zim. He's your ally, we are all soldiers here and that includes you." Said Shepard. "_Fool _Zim is part of nothing and works for no one. Not since the tallest betrayed me."

"Well you know it's not my job to keep you alive. I could throw you out the air lock right now. I'm going to bring you with me on a mission and if you don't help out, I'll leave you behind. Instead of going over all the basics of our galaxy I'll give you this codex. Now you have no excuse to not understand something on our ship." Said Shepard as he walked out of the room.

"Wait! Shepard- human, you can't leave me with this four eyed stink beast!" said Zim. Shepard ignored this and continued to walk out. For a few hours Zim paced around and mumbled in anger, Javik just stood and washing his hands.

Eventually Javik stopped what he was doing and walked over to Zim and picked him up by his uniform's neck. "I've had to deal with many of my own kind like you and I've learned to ignore but, you are beginning to interfere with my meditation." Said Javik.

"Wait, you meditate by washing your hands?" asked Zim. "Yes , and I can no longer focus with your constant ranting." Said Javik sternly. "How dare you tell me what to do you four eyed stink beast!" Javik's look changed when Zim said that and he began to glow green. "You insult the Protheans!" shouted Javik.

Meanwhile Shepard sat in his quarters poking the husks head he recovered from the Citadel. Suddenly Shepard could hear Jokers voice over the loudspeaker. "Uhhh Commander, it looks like theirs some commotion with Javik and that new little green guy." Shepard sighed and headed to the elevator.

When Shepard arrived in the engineering deck he could hear the explosions coming from port cargo. He started to run to port cargo to find out what was going on. When Shepard opened the door to port cargo he could see Javik blasting green biotics at Zim. Zim was using four metal spider legs from his PAK to crawl across the ceiling and return fire.

"Hey! Break it up you two." Said Shepard in an annoyed tone. "Commander, this thing insults me and all other protheans. Either you take him out of here or I will kill him." Shepard hesitated for a moment. He knew there was only one place Zim could go where he wouldn't cause trouble.

Shepard's own quarters. "Zim. Come with me, now." Said Shepard in a very annoyed tone. Zim crawled down and retracted his metal spider legs. Zim followed Shepard out of port cargo, as he left he stuck out his tongue at Javik.

"Where are we going?" Zim asked as Shepard and Zim entered the elevator. "The only place I have left to put you. You know, the only reason I've decided to keep you alive is because of what I just saw in their. If you can save all that rage for the reapers then I think you might be a powerful ally."

"Think? I am amazing! I will crush the burrito monsters!" Finally the elevator opened and Zim was shocked to see such a nice looking cabin. "Wow! This is my new room! Ha that stupid four eyed beast!" said Zim. "No. You get the couch, and don't touch anything."

Right after that Zim ran over to Shepards model ships. "Say, can I use these for scrap metal? Or wait, can I experiment on this hamster? Shepard winced. He didn't know what he would do if anyone touched his precious hamster. Once Zim was done there he ran over to Shepards husk head.

"Say, this looks like Dib, wait, nevermind it's heads not big enough. Owww! It bit me." "Zim! Just sit down and be quiet. I have things to do and I don't need anymore trouble from you." Said Shepard. Zim just stared and looked as innocent as possible.

Shepard raised a finger, as if he was going to say more but he just sighed and left Zim sitting on the couch. "Wait! One last thing." Said Shepard. He picked up a holographic codex tablet and threw it to Zim and then Shepard finally left.

Shepard then went to the galaxy map and headed for one of the planets where there were Irken Elites pinned down by the reapers. He headed back up to his cabin to get Zim for the mission only to find his model Citadel gone and his hamster cage broken and Zim, nowhere to be found. Shepard opened up the bathroom door only to see his beloved space hamster, now eight times bigger and Zim sitting with goggles on welding something together.

Zim paused for a minute. Then turned on whatever it was he was creating. The little robot stood up and began to speak in an incredibly annoying high pitched voice. "MASTER!" said the little robot with joy. "Well I'm glad I saved Gir's memory core." Said Zim.

Shepard again raised his finger and glared but just sighed and walked off. He walked to his bed and collapsed into a pillow. "Joker can you please keep Zim in the bridge for a while. Just so I can get some sleep." Said Shepard muffled by the pillow.

Joker responded over the loudspeaker. "Aw you have gotta be kidding me. He's got a little robot sidekick now." Joker sighed and agreed to take Zim and the little robot while Shepard slept. Shepard then drifted off to sleep with his face buried in his pillow.

He noticed a familiar nightmare, this time though he could faintly hear Zim laughing. Shepard chased the little boy around like he usually did in nightmares but this time when he caught up to the boy he noticed his outfit changed to a red striped uniform with black gloves and boots. He only had three fingers and his skin turned green. Antennae grew on the boys head and when he looked up at Shepard he could see that the boy was now Zim. Zim began to give Shepard an evil look and laughed his usual evil laugh. Just then Shepard gasped and woke up to see Zim poking him and saying wake up.

Shepard just sighed.

**A.N. **

**Well at least now I could start adding in some humor. Not as funny as I hoped it would be but still pretty funny!**


	3. Chapter 3

Rain pours down and lightning flashes across the pitch black sky. A faint sparkle of light is seen off in the distance and an Alliance shuttle emerges from the darkness and speeds through the storm and eventually stops at the base of a cliff.

The door slides open and Shepard is holding on to Zim by the back and throws him out almost immediately after the door opens and shoots him a stern glare.

"They're your people, you save them. I'm sending the coordinates for the extraction point to your new omni tool. I hope you learned how to use it because we're only waiting ten minutes for you before we leave. We'll extract you at exactly 0400 hours tomorrow."

Zim simply looked back at Shepard resentfully as the door slammed shut and the shuttle flew off. He stood motionless for a moment but after a few moments he looked at his wrist and it lit up with the bright yellow light of an omni tool.

Luckily Zim's kinetic barriers which he also received recently shielded his skin from the rain. He pressed a few buttons on it and immediately after a bright light was shot out from the base of the omni tool. He walked up the side of the mountain for about an hour and a half until he paused for a moment when he thought he heard something moving in the distance.

Zim shined his light toward the source of the noise and heard something scurry away. He tried desperately to follow the noise but he failed and was ambushed by a husk. The husk quickly overpowered Zim and it had him on the ground in seconds.

Just as the husk was about to bite into Zim's flesh one of his spider legs extended from his PAK and it impaled the husk and threw it off of him. Zim then stood up and brushed himself off and continued up the mountain.

Another hour later Zim reached the peak of the mountain and looked for a nice vantage point. Once he found a decent place to scout a metal arm with a pair of night vision binoculars emerged from his PAK. After searching for a few minutes he realized that even night vision was not enough to see through this rain.

"Switch to thermal." said Zim. Just then the view inside the binoculars changed to a thermal view so that he could see any sources of heat. Eventually he spotted a large mass of enemies and further on a fortification with a group of snipers. It was difficult for Zim to tell but they appeared Irken to him.

He pondered for a few moments thinking about what to do. He decided he would have GIR fly down the mountainside and distract the enemies while he evacuated the elites.

"Ah, I'm running low on ammunition." Said one of the four elites. "Sorry we're all pretty low here." Said another elite. They were each sure of their death already having lost two men to banshees. Husks charged toward their barricade and their was little the elites could to because of their dwindling ammo supply.

Suddenly as the husks were not more than 20 feet away from the barricade they were blown back by the explosion from a small SIR unit crashing down into the husks. The SIR unit's eyes glowed red and a large arsenal of weapons emerged from it's head.

It blasted hundreds of missiles and bullets toward the husks, cannibals, banshees, and brutes and one by one they fell. The elites took this opportunity to sneak away from the barricade and move in the other direction.

One of the elites heard something moving off in the brush and searched through it finding Zim. The elite pointed his gun at him and when Zim noticed this he put his hands up.

"Wait, don't shoot. I'm here to extract you!" said Zim. Soon all four elites came over to see what had happened. "Really? You? Here to extract us? Well we have a hard time trusting shit heads like you. It's almost more dangerous to be your ally then your enemy." Said the elite pointing his gun at Zim.

"I'm not here because I want to be, I'm hear under orders of the human Commander Shepard." Replied Zim. "Oh, yeah. That's right the Tallest decided to enlist you with the human alliance so they could finally be rid of you. Well we don't trust you, but if you have a way off this hellhole then we'll follow you." Said the elite lowering his gun.

Commander Shepard looked at the UAV transmission that he sent to tag Zim so he could monitor his progress and after he had spent the last few hours watching it he switched it off when Joker called him on the loudspeaker.

"Commander, urgent transmission coming in from Admiral Hackett, it's about the Irken Armada." Said Joker. Shepard tossed down the datapad he was using as a monitor for the UAV transmission and sat up from his couch in his cabin and headed to the elevator.

"Commander. The Irkens are ready to officially join the summit but their was a few issues with their home planet the Tallest wanted to discuss with you on your ship. Strange race, who chooses their leaders based on height? If that were the case with us we'd probably never have the alliance because the idiots in charge wouldn't be smart enough to come up with it. If the Tallest really aren't idiots then they'll give us the full support of their fleet. However I don't think we can get them to help much with the crucible. Well at least they can share their large stockpile of snacks with the engineers working on the crucible. By the way, how's that operative they assigned you working out?"

Shepard sighed. "You don't want to know sir . . ." replied Shepard. "Well, your probably right about that, I'm glad you're the one dealing with the Irkens and not me, I can't stand being around them, maybe it's the name. Hackett out."

Later Shepard suited up and prepared to head off in the shuttle to pick up Zim and the elites. Once the shuttle reached the surface Shepard opened up the doors and looked around, there was no one in site. After a few moments Zim came into view and he ran up to the shuttle and threw a disabled GIR into the shuttle.

"Where's the elites Zim? You were supposed to pick them up remember?" asked Shepard. "I used them as a distraction so I could make a break for the shuttle. They didn't know that though." Suddenly Shepard glared and just could help but punch Zim in the face.

"HEY! What was that for?" said Zim startled by Shepard's fist hitting his face. "Your putting innocent lives at stake so you can save _yourself_. I'm coming with you and we're going to get every one of those elites before we leave here, is that understood soldier!" Zim said nothing at this and followed Shepard.

Not long after Shepard and Zim save the elites and brought them to the shuttle, there was only three. "We lost a man because of that lunatic!" said one of the elites as Shepard was loading them onto the shuttle. They were all severely injured.

When Shepard heard this he punched Zim again, this time sending him to the ground. Shepard no longer had anything to say to Zim and simply looked down in shame. Shepard didn't realize it but a banshee silently crept behind him. Zim noticed this but did not warn Shepard.

Shepard turned around startled and tried to evade but he wasn't quick enough and soon the banshee had him by the neck. Shepard closed his eyes shut certain he would die. He heard a snap and quickly opened his eyes and notice a metal spider leg impaled through the banshees head.

It was Zim's spider leg. Shepard was surprised Zim would save him because of his nature but that still didn't redeem him to Shepard. They did not speak to each other once for the entire shuttle ride to the Normandy.


	4. NIGHTMARE

**NIGHTMARE**

Shepard stepped through the elevator into his cabin, he wasn't eager to return to return to his nightmares but after the events that had occurred all he wanted to do was rest. He climbed onto the bed and tried to quiet his mind and drift off to sleep.

To Shepards surprise he was in an unfamiliar setting. The place he was at was closer looking to Tuchanka than his usual nightmare setting. He looked around for a moment and soon he was in a clearing standing across from Zim.

A blank look engulfed Zim's face and he said nothing. He simply stared blankly at him and extended his spider legs and charged at Shepard. Shepard moved out of the way in time to dodge Zim but as Zim turned around and looked back at Shepard with the same blank look he evaporated.

In Zim's place was an M6 Carnifex heavy pistol. Shepard walked over to it and picked it up. He would soon need it because reaper forces began to pour in out of nowhere.

Wave after wave Shepard wiped out the reaper forces and after awhile he found himself struggling against the reaper forces which were now overwhelming him. Shepard ducked back down into cover and reloaded his pistol.

As he did this there was a break in the enemies fire. Shepard looked around but all of the reaper forces had appeared to have vanished. Suddenly three reaper destroyers crashed into the ground. Hundreds of Irken fighters and voot runners swarmed around the trio of destroyers.

This was all in vain however as Shepard watched the reapers decimate the small Irken ships. The reaper in the middle of the trio began to fire it's laser at Shepard. He ran desperately from place to place seeking cover from the blasts. This reaper didn't drag it's laser toward Shepard like other reapers had. This one simply pointed and shot. Nearly hitting Shepard every time.

Soon the other two destroyers had dealt with the insignificant Irken fighters and began firing at Shepard as well in the same way the first one had. After a few minutes of helpless running from the blast Shepard saw a very large reddish object in the sky.

It was probably 5 miles long. After it came into clearer view Shepard realized it was the massive itself. A band on the front of it lit up with a light so bright it nearly blinded Shepard. Seconds later a blast of energy larger than all three of the reapers landed directly over them. The blast was so large that it consumed Shepard after a few moments.

Shepard soon found himself back in his familiar dreamscape but this time Zim stood next to him. The same blank look across his face. Instead of seeing the boy another reaper destroyer stood in front of Shepard and Zim.

It growled at them. Shepard fired his pistol three times at the destroyer and as Shepard prepared to run at it one of Zim's spider legs went over Shepards shoulder and he looked back at Zim who still had a blank look but nodded in disagreement at Shepards actions.

Zim extended all of his spider legs and crawled at an extremely fast pace towards the towering destroyer. Zim leaped up towards the projector of the reaper's lase and threw out one of his spider legs at it.

The entire time he kept the same blank look. As Zim's spider leg hit the eye of the reaper a bright light engulfed the area and Zim and the reaper were gone. Now Shepard saw the boy he was familiar with and followed him through the forest.

Once Shepard caught up with the boy he turned around and spoke to Shepard. "Please, save me from that creature." As the boy said this he pointed behind Shepard. Shepard looked back and was shocked to see Zim.

Zim still had the same blank look on his face. Zim extended two spider legs and ran towards the child. Shepard jumped in front of Zim and Zim stabbed him in the gut and threw him out of the way. Just as Zim was about to strike the boy everything went white.

"Your mind belongs to me. It is pointless to resist. You will serve us." Said Harbinger just before Shepard awoke and gasped for air.


End file.
